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Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics is Highly Beneficial.

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Input data

Alignments are provided in PHYLYP sequential format, followed by DSSP secondary-structure and solvent-exposure annotations , using Stockholm format. PhyML-structure simplifies these annotations by:

1. Secondary structure: E (extended or E in DSSP), H (helix or H in DSSP), and other structures S, T, B, G, I, C, ".", "X", or "?" in DSSP. PhyML-structure regards structures differing from E and H as other (O). X and ? correspond to unknown values and are dealt with using a mixture (with CONF/MIX) or LG (with CONF/LG and PART).
2. Classifying the sites into 10 relative surface accessibility categories: [0-9X] where (0=0%-10%; ...; 9=90%-100%). PhyML-structure considers 0 as buried values and [1-9] as exposed values.
3. Following Stockholm format, Secondary Structure and Surface Accessibility notations are coded by

        #=GR  SS        Secondary Structure    For protein [HGIEBTSCX]
        #=GR  SA        Surface Accessibility  [0-9X]  (0=0%-10%; ...; 9=90%-100%)
   

   In the provided alignments, we include secondary structure information, surface accessibility, and original solvent exposure values.

See example.

Model

Amino-acid based models : EX2 (default) | EX3 | EHO | EX_EHO |UL2 | UL3 | LG | WAG | JTT

• EX2: two-matrix model corresponding to exposed/buried sites.
• EX3: three-matrix model corresponding to highly exposed/intermediate/buried sites*.
• EHO: three-matrix model corresponding to extended/helix/other sites.
• EX_EHO: six-matrix model corresponding to exposed/buried and extended/helix/other sites.

• UL2: two-matrix model learned by unsupervised data*.
• UL3: three-matrix model learned by unsupervised data*.

(*) We could extract three rate categories of EX3 by cutting relative solvent exposure values as [0-.08], [0.08-0.36] and [0.36 –1] for S (slow), M (medium) and F (fase).
See Le S.Q, Lartillot N. Gascuel O. (2008).
Phylogenetic Mixture Models for Proteins,
Philosophical Transactions of the Royal Society B, Vol. 363 (1512), 3965-3976.

Mode

• CONF/MIX: combination of PART and MIX with confidence leve c. We apply cPART + (1-c) MIX to sites with structure information and MIX to sites without structure information. The stat output file includes c and information of MIX (see example for more detail).
• CONF/LG: combination of PART and LG with confidence leve c. We apply cPART + (1-c) LG to sites with structure information and MIX to sites without structure information. The stat output file includes c (see example for more detail).
• PART: We apply the corresponding models for sites with structure information and LG to sites without structure information (see example for more detail).
• MIX: We apply MIX to all sites. The stat output file includes information of MIX (see example for more detail).

Running PhyML-structure

phyml-structure [command args]

Command options:

• --help: instructions
• -i (or --input) seq_file_name
  seq_file_name is the name of the nucleotide or amino-acid sequence file in PHYLIP format.
• -b (or --bootstrap) int
  • int > 0 : int is the number of bootstrap replicates.
  • int = 0 : neither approximate likelihood ratio test nor bootstrap values are computed.
  • int = -1 : approximate likelihood ratio test returning aLRT statistics.
  • int = -2 : approximate likelihood ratio test returning Chi2-based parametric branch supports.
  • int = -3 : minimum of Chi2-based parametric and SH-like branch supports.
  • int = -4 : SH-like branch supports alone (default).
• -m (or --model) model
  model : substitution model name.
  Amino-acid based models : EX2 (default) | EX3 | EHO | EX_EHO |UL2 | UL3 | LG | WAG | JTT
  • EX2: two-matrix model corresponding to exposed/buried sites.
  • EX3: three-matrix model corresponding to highly exposed/intermediate/buried sites.
  • EHO: three-matrix model corresponding to extended/helix/other sites.
  • EX_EHO: six-matrix model corresponding to exposed/buried and extended/helix/other sites.
    
    
  • UL2: two-matrix model learned by unsupervised data.
  • UL3: three-matrix model learned by unsupervised data.
  See Le S.Q, Lartillot N. Gascuel O. (2008).
  Phylogenetic Mixture Models for Proteins,
  Philosophical Transactions of the Royal Society B, Vol. 363 (1512), 3965-3976.
• -M: mode [PART] [MIX] [CONF/MIX] [CON/LG]
  
  • PART: Partitioning models. LG is used for sites with missing structure notations
  • MIX : Mixture models
  • CONF/MIX: confidence-based model, using MIX for poorly annotated sites
  • CONF/LG : confidence-based model, using LG for poorly annotated sites
  Default: CONF/MIX when alignments have structure information.
• -y:
  Alignments are provided in PHYLYP sequential format, followed by DSSP secondary-structure and solvent-exposure annotations , using Stockholm format. PhyML-structure simplifies these annotations by:
  1. Secondary structure: E (extended or E in DSSP), H (helix or H in DSSP), and other structures S, T, B, G, I, C, ., X, or ? in DSSP. PhyML-structure regards structures differing from E and H as other (O). X and ? correspond to unknown values and are dealt with using a mixture (with CONF/MIX) or LG (with CONF/LG and PART).
  2. Classifying the sites into 10 relative surface accessibility categories: [0-9X] where (0=0%; ...; 9=90%). PhyML-structure considers 0 as buried values and [1-9] as exposed values.
  3. Following Stockholm format, Secondary Structure and Surface Accessibility notations are coded by

          #=GR  SS        Secondary Structure    For protein [HGIEBTSCX]
          #=GR  SA        Surface Accessibility  [0-9X]  (0=0%-10%; ...; 9=90%-100%)
     

• -v (or --pinv) prop_invar
  prop_invar : proportion of invariable sites.
  Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate. Default [v = 0].
• -c (or --nclasses) nb_subst_cat
  nb_subst_cat : number of relative substitution rate categories. Default : [nb_subst_cat=4].
  Must be a positive integer.
• -a (or --alpha) gamma
  gamma : distribution of the gamma distribution shape parameter.
  Can be a fixed positive value or e to get the maximum likelihood estimate. Default [e].
• -s (or --search) move
  Tree topology search operation option.
  Can be either NNI (default) or SPR.
• -u (or --inputtree) user_tree_file
  user_tree_file : starting tree filename. The tree must be in Newick format.
• -o params
  This option focuses on specific parameter optimisation.
  • params=tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
  • params=tl : tree topology and branch length are optimised.
  • params=lr : branch length and rate parameters are optimised.
  • params=l : branch length are optimised.
  • params=r : rate parameters are optimised.
  • params=n : no parameter is optimised.
• --rand_start
  This option sets the initial tree to random.
  It is only valid if SPR searches are to be performed.
• --n_rand_starts num
  num is the number of initial random trees to be used.
  It is only valid if SPR searches are to be performed.
• --r_seed num
  num is the seed used to initiate the random number generator.
  Must be an integer.
• --print_site_lnl
  Print the likelihood for each site in file *_phyml_lk.txt.
• --print_trace
  Print each phylogeny explored during the tree search process in file *_phyml_trace.txt.

PHYLIP-Like interface

You can use phyml with no arguments, in this case change the value of a parameter by typing its corresponding character as shown on screen.

Examples

    ./PhyML-SS -i Ord0300_2hhi.STR -m EX2 -M PART -c 4 -a e

Contact: Vincent Lefort, LIRMM.